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SCFD2 sec1 family domain containing 2 [ Homo sapiens (human) ]

Gene ID: 152579, updated on 5-Mar-2024

Summary

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Official Symbol
SCFD2provided by HGNC
Official Full Name
sec1 family domain containing 2provided by HGNC
Primary source
HGNC:HGNC:30676
See related
Ensembl:ENSG00000184178 AllianceGenome:HGNC:30676
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
STXBP1L1
Summary
Predicted to enable syntaxin binding activity. Predicted to be involved in intracellular protein transport and vesicle docking involved in exocytosis. Predicted to be active in plasma membrane and secretory granule. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 1.5), adrenal (RPKM 1.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
4q12
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (52872982..53366061, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (56359861..56853303, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (53739149..54232228, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15428 Neighboring gene uncharacterized LOC124900700 Neighboring gene Sharpr-MPRA regulatory region 13979 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:53733886-53734386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:53734387-53734887 Neighboring gene NANOG hESC enhancer GRCh37_chr4:53739270-53739771 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:53739925-53740884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:53743608-53744108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21558 Neighboring gene RAS like family 11 member B Neighboring gene uncharacterized LOC101928658 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:53816447-53817384 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21559 Neighboring gene uncharacterized LOC124900701 Neighboring gene VISTA enhancer hs1668 Neighboring gene VISTA enhancer hs1460 Neighboring gene NANOG hESC enhancer GRCh37_chr4:54102933-54103444 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:54103445-54103956 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:54122352-54122863 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:54140029-54140243 Neighboring gene RNA, U6 small nuclear 310, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:54195258-54195835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21562 Neighboring gene uncharacterized LOC105377654 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:54243526-54244074 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:54244075-54244623 Neighboring gene factor interacting with PAPOLA and CPSF1 Neighboring gene LNX1 antisense RNA 1 Neighboring gene ligand of numb-protein X 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. PSF Promotes ER-Positive Breast Cancer Progression via Posttranscriptional Regulation of ESR1 and SCFD2. Mitobe Y, et al. Cancer Res, 2020 Jun 1. PMID 32213542
  2. PSPC1 is a potential prognostic marker for hormone-dependent breast cancer patients and modulates RNA processing of ESR1 and SCFD2. Takeiwa T, et al. Sci Rep, 2022 Jun 9. PMID 35681031, Free PMC Article
  3. Genome-wide association identifies ATOH7 as a major gene determining human optic disc size. Macgregor S, et al. Hum Mol Genet, 2010 Jul 1. PMID 20395239, Free PMC Article
  4. Genome-wide association study of smoking behaviours in patients with COPD. Siedlinski M, et al. Thorax, 2011 Oct. PMID 21685187, Free PMC Article
  5. FAM105A/OTULINL Is a Pseudodeubiquitinase of the OTU-Class that Localizes to the ER Membrane. Ceccarelli DF, et al. Structure, 2019 Jun 4. PMID 31056421, Free PMC Article

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PSPC1 is a potential prognostic marker for hormone-dependent breast cancer patients and modulates RNA processing of ESR1 and SCFD2.
    Title: PSPC1 is a potential prognostic marker for hormone-dependent breast cancer patients and modulates RNA processing of ESR1 and SCFD2.
  2. PSF Promotes ER-Positive Breast Cancer Progression via Posttranscriptional Regulation of ESR1 and SCFD2.
    Title: PSF Promotes ER-Positive Breast Cancer Progression via Posttranscriptional Regulation of ESR1 and SCFD2.
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association identifies ATOH7 as a major gene determining human optic disc size.
EBI GWAS Catalog
Genome-wide association study of smoking behaviours in patients with COPD.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ21060, FLJ39514

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
  

General protein information

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Preferred Names
sec1 family domain-containing protein 2
Names
syntaxin binding protein 1-like 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_152540.4 → NP_689753.2  sec1 family domain-containing protein 2

    See identical proteins and their annotated locations for NP_689753.2

    Status: VALIDATED

    Source sequence(s)
    AY299407
    Consensus CDS
    CCDS33984.1
    UniProtKB/Swiss-Prot
    Q8N5F3, Q8N8H0, Q8WU76, Q96ED3
    Related
    ENSP00000384182.3, ENST00000401642.8
    Conserved Domains (1) summary
    cl15415
    Location:572 → 665
    Sec1; Sec1 family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    52872982..53366061 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007787.3 → XP_016863276.1  sec1 family domain-containing protein 2 isoform X4

  2. XM_047449646.1 → XP_047305602.1  sec1 family domain-containing protein 2 isoform X2

  3. XM_017007786.3 → XP_016863275.1  sec1 family domain-containing protein 2 isoform X1

  4. XM_011534376.4 → XP_011532678.1  sec1 family domain-containing protein 2 isoform X5

  5. XM_011534375.4 → XP_011532677.1  sec1 family domain-containing protein 2 isoform X3

  6. XM_047449647.1 → XP_047305603.1  sec1 family domain-containing protein 2 isoform X7

  7. XM_011534378.4 → XP_011532680.1  sec1 family domain-containing protein 2 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    56359861..56853303 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348996.1 → XP_054204971.1  sec1 family domain-containing protein 2 isoform X4

  2. XM_054348994.1 → XP_054204969.1  sec1 family domain-containing protein 2 isoform X2

  3. XM_054348993.1 → XP_054204968.1  sec1 family domain-containing protein 2 isoform X1

  4. XM_054348997.1 → XP_054204972.1  sec1 family domain-containing protein 2 isoform X5

  5. XM_054348995.1 → XP_054204970.1  sec1 family domain-containing protein 2 isoform X3

  6. XM_054348999.1 → XP_054204974.1  sec1 family domain-containing protein 2 isoform X7

  7. XM_054348998.1 → XP_054204973.1  sec1 family domain-containing protein 2 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WU76.2 GenPept UniProtKB/Swiss-Prot:Q8WU76

Gene LinkOut

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